EHV-1 TSS dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TSS dynamics
Those reads were counted only, where the 5-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.## Bootstrap (r = 0.59)... Done.## Bootstrap (r = 0.7)... Done.## Bootstrap (r = 0.8)... Done.## Bootstrap (r = 0.9)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.09)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.29)... Done.## Bootstrap (r = 1.39)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.## Bootstrap (r = 0.58)... Done.## Bootstrap (r = 0.69)... Done.## Bootstrap (r = 0.77)... Done.## Bootstrap (r = 0.88)... Done.## Bootstrap (r = 1.0)... Done.## Bootstrap (r = 1.08)... Done.## Bootstrap (r = 1.19)... Done.## Bootstrap (r = 1.27)... Done.## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 1 ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13: 1 ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14: 1 ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16: 1 ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17: 1 ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19: 1 NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 2 ORF8 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31: 2 ORF22 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32: 2 ORF23 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33: 2 ORF24 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34: 2 ORF25 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36: 2 ORF27 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37: 2 ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39: 2 ORF32 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 40: 2 ORF33 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 41: 2 ORF35.5 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 42: 2 ORF36 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 43: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 44: 2 ORF39 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 45: 2 CTO 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 46: 2 ORF40 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 47: 2 ORF42 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 48: 2 ORF43 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 49: 2 ORF44 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 50: 2 ORF46 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 51: 2 ORF49 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 52: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 53: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 54: 2 ORF58 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 55: 2 ORF59 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 56: 2 ORF62 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 57: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 58: 2 ORF68 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 59: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 60: 2 ORF74 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 61: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 62: 3 ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 63: 3 ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 64: 4 ORF12 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 65: 4 ORF13 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 66: 4 ORF15 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 67: 4 ORF16 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 68: 4 ORF35 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 69: 4 ORF41 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 70: 4 ORF45 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 71: 4 ORF48 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 72: 4 ORF52 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 73: 4 ORF54 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 74: 4 ORF57 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 75: 4 ORF60 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 76: 4 ORF71 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 77: 4 ORF72 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 78: 5 ORF64_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 79: 5 ORF75 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.005027291 -1.1453678 0.6808478 0.04001638
## 40: 0.005027291 -1.1453678 0.6808478 0.04001638
## 41: 0.005027291 -1.1453678 0.6808478 0.04001638
## 42: 0.005027291 -1.1453678 0.6808478 0.04001638
## 43: 0.005027291 -1.1453678 0.6808478 0.04001638
## 44: 0.005027291 -1.1453678 0.6808478 0.04001638
## 45: 0.005027291 -1.1453678 0.6808478 0.04001638
## 46: 0.005027291 -1.1453678 0.6808478 0.04001638
## 47: 0.005027291 -1.1453678 0.6808478 0.04001638
## 48: 0.005027291 -1.1453678 0.6808478 0.04001638
## 49: 0.005027291 -1.1453678 0.6808478 0.04001638
## 50: 0.005027291 -1.1453678 0.6808478 0.04001638
## 51: 0.005027291 -1.1453678 0.6808478 0.04001638
## 52: 0.005027291 -1.1453678 0.6808478 0.04001638
## 53: 0.005027291 -1.1453678 0.6808478 0.04001638
## 54: 0.005027291 -1.1453678 0.6808478 0.04001638
## 55: 0.005027291 -1.1453678 0.6808478 0.04001638
## 56: 0.005027291 -1.1453678 0.6808478 0.04001638
## 57: 0.005027291 -1.1453678 0.6808478 0.04001638
## 58: 0.005027291 -1.1453678 0.6808478 0.04001638
## 59: 0.005027291 -1.1453678 0.6808478 0.04001638
## 60: 0.005027291 -1.1453678 0.6808478 0.04001638
## 61: 0.005027291 -1.1453678 0.6808478 0.04001638
## 62: 0.004876780 -1.6233205 0.9970391 0.31825293
## 63: 0.004876780 -1.6233205 0.9970391 0.31825293
## 64: 0.004864578 -1.8164413 1.1545088 0.27283204
## 65: 0.004864578 -1.8164413 1.1545088 0.27283204
## 66: 0.004864578 -1.8164413 1.1545088 0.27283204
## 67: 0.004864578 -1.8164413 1.1545088 0.27283204
## 68: 0.004864578 -1.8164413 1.1545088 0.27283204
## 69: 0.004864578 -1.8164413 1.1545088 0.27283204
## 70: 0.004864578 -1.8164413 1.1545088 0.27283204
## 71: 0.004864578 -1.8164413 1.1545088 0.27283204
## 72: 0.004864578 -1.8164413 1.1545088 0.27283204
## 73: 0.004864578 -1.8164413 1.1545088 0.27283204
## 74: 0.004864578 -1.8164413 1.1545088 0.27283204
## 75: 0.004864578 -1.8164413 1.1545088 0.27283204
## 76: 0.004864578 -1.8164413 1.1545088 0.27283204
## 77: 0.004864578 -1.8164413 1.1545088 0.27283204
## 78: 0.004541086 -0.4455417 1.1235184 0.24166784
## 79: 0.004541086 -0.4455417 1.1235184 0.24166784
## se.bp v c pchi
## [1] "ORF67_1" "ORF32" "ORF58" "ORF33" "ORF35.5" "ORF25" "ORF27"
## [8] "ORF62"## [1] 8## [1] "ORF64_1" "ORF75"## [1] 2Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 1 ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13: 1 ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14: 1 ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16: 1 ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17: 1 ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19: 1 NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31: 2 ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39: 3 ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 40: 3 ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 41: 4 ORF8 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 42: 4 ORF22 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 43: 4 ORF23 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 44: 4 ORF24 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 45: 4 ORF25 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 46: 4 ORF27 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 47: 4 ORF32 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 48: 4 ORF33 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 49: 4 ORF35.5 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 50: 4 ORF36 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 51: 4 ORF39 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 52: 4 CTO 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 53: 4 ORF40 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 54: 4 ORF42 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 55: 4 ORF43 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 56: 4 ORF44 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 57: 4 ORF46 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 58: 4 ORF49 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 59: 4 ORF58 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 60: 4 ORF59 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 61: 4 ORF62 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 62: 4 ORF68 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 63: 4 ORF74 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 64: 5 ORF12 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 65: 5 ORF13 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 66: 5 ORF15 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 67: 5 ORF16 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 68: 5 ORF35 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 69: 5 ORF41 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 70: 5 ORF45 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 71: 5 ORF48 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 72: 5 ORF52 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 73: 5 ORF54 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 74: 5 ORF57 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 75: 5 ORF60 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 76: 5 ORF71 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 77: 5 ORF72 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 78: 6 ORF64_1 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 79: 6 ORF75 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.004876780 -1.6233205 0.9970391 0.31825293
## 40: 0.004876780 -1.6233205 0.9970391 0.31825293
## 41: 0.004864578 -1.8164413 1.1545088 0.27283204
## 42: 0.004864578 -1.8164413 1.1545088 0.27283204
## 43: 0.004864578 -1.8164413 1.1545088 0.27283204
## 44: 0.004864578 -1.8164413 1.1545088 0.27283204
## 45: 0.004864578 -1.8164413 1.1545088 0.27283204
## 46: 0.004864578 -1.8164413 1.1545088 0.27283204
## 47: 0.004864578 -1.8164413 1.1545088 0.27283204
## 48: 0.004864578 -1.8164413 1.1545088 0.27283204
## 49: 0.004864578 -1.8164413 1.1545088 0.27283204
## 50: 0.004864578 -1.8164413 1.1545088 0.27283204
## 51: 0.004864578 -1.8164413 1.1545088 0.27283204
## 52: 0.004864578 -1.8164413 1.1545088 0.27283204
## 53: 0.004864578 -1.8164413 1.1545088 0.27283204
## 54: 0.004864578 -1.8164413 1.1545088 0.27283204
## 55: 0.004864578 -1.8164413 1.1545088 0.27283204
## 56: 0.004864578 -1.8164413 1.1545088 0.27283204
## 57: 0.004864578 -1.8164413 1.1545088 0.27283204
## 58: 0.004864578 -1.8164413 1.1545088 0.27283204
## 59: 0.004864578 -1.8164413 1.1545088 0.27283204
## 60: 0.004864578 -1.8164413 1.1545088 0.27283204
## 61: 0.004864578 -1.8164413 1.1545088 0.27283204
## 62: 0.004864578 -1.8164413 1.1545088 0.27283204
## 63: 0.004864578 -1.8164413 1.1545088 0.27283204
## 64: 0.004541086 -0.4455417 1.1235184 0.24166784
## 65: 0.004541086 -0.4455417 1.1235184 0.24166784
## 66: 0.004541086 -0.4455417 1.1235184 0.24166784
## 67: 0.004541086 -0.4455417 1.1235184 0.24166784
## 68: 0.004541086 -0.4455417 1.1235184 0.24166784
## 69: 0.004541086 -0.4455417 1.1235184 0.24166784
## 70: 0.004541086 -0.4455417 1.1235184 0.24166784
## 71: 0.004541086 -0.4455417 1.1235184 0.24166784
## 72: 0.004541086 -0.4455417 1.1235184 0.24166784
## 73: 0.004541086 -0.4455417 1.1235184 0.24166784
## 74: 0.004541086 -0.4455417 1.1235184 0.24166784
## 75: 0.004541086 -0.4455417 1.1235184 0.24166784
## 76: 0.004541086 -0.4455417 1.1235184 0.24166784
## 77: 0.004541086 -0.4455417 1.1235184 0.24166784
## 78: 0.005235761 -1.1178069 0.8390202 0.58404011
## 79: 0.005235761 -1.1178069 0.8390202 0.58404011
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF32" "ORF62" "ORF45"## [1] 6## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF45" "ORF48" "ORF52"
## [10] "ORF54" "ORF57" "ORF60" "ORF71" "ORF72"## [1] 14Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF4 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF7 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF9 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF20 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF21 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 ORF31 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 1 ORF34 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 13: 1 ORF38 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 14: 1 ORF50 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 15: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 16: 1 ORF56 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 17: 1 ORF61 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 18: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 19: 1 NOIR_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 20: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 21: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 22: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 23: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 24: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 27: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 28: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 29: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 30: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 31: 2 ORF28 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 32: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 33: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 34: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 35: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 36: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 37: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 38: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 39: 3 ORF6 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 40: 3 ORF70 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 41: 4 ORF8 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 42: 4 ORF22 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 43: 4 ORF23 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 44: 4 ORF24 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 45: 4 ORF25 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 46: 4 ORF27 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 47: 4 ORF32 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 48: 4 ORF33 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 49: 4 ORF35.5 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 50: 4 ORF36 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 51: 4 ORF39 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 52: 4 CTO 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 53: 4 ORF40 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 54: 4 ORF42 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 55: 4 ORF43 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 56: 4 ORF44 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 57: 4 ORF46 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 58: 4 ORF49 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 59: 4 ORF58 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 60: 4 ORF59 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 61: 4 ORF62 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 62: 4 ORF68 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 63: 4 ORF74 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 64: 5 ORF12 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 65: 5 ORF13 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 66: 5 ORF15 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 67: 5 ORF16 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 68: 5 ORF35 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 69: 5 ORF41 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 70: 5 ORF48 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 71: 5 ORF52 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 72: 5 ORF54 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 73: 5 ORF57 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 74: 5 ORF60 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 75: 5 ORF71 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 76: 5 ORF72 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 77: 6 ORF45 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 78: 7 ORF64_1 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 79: 7 ORF75 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.004437298 -1.8423439 0.9718909 0.80502549
## 13: 0.004437298 -1.8423439 0.9718909 0.80502549
## 14: 0.004437298 -1.8423439 0.9718909 0.80502549
## 15: 0.004437298 -1.8423439 0.9718909 0.80502549
## 16: 0.004437298 -1.8423439 0.9718909 0.80502549
## 17: 0.004437298 -1.8423439 0.9718909 0.80502549
## 18: 0.004437298 -1.8423439 0.9718909 0.80502549
## 19: 0.004437298 -1.8423439 0.9718909 0.80502549
## 20: 0.004437298 -1.8423439 0.9718909 0.80502549
## 21: 0.004437298 -1.8423439 0.9718909 0.80502549
## 22: 0.004437298 -1.8423439 0.9718909 0.80502549
## 23: 0.004437298 -1.8423439 0.9718909 0.80502549
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.005027291 -1.1453678 0.6808478 0.04001638
## 27: 0.005027291 -1.1453678 0.6808478 0.04001638
## 28: 0.005027291 -1.1453678 0.6808478 0.04001638
## 29: 0.005027291 -1.1453678 0.6808478 0.04001638
## 30: 0.005027291 -1.1453678 0.6808478 0.04001638
## 31: 0.005027291 -1.1453678 0.6808478 0.04001638
## 32: 0.005027291 -1.1453678 0.6808478 0.04001638
## 33: 0.005027291 -1.1453678 0.6808478 0.04001638
## 34: 0.005027291 -1.1453678 0.6808478 0.04001638
## 35: 0.005027291 -1.1453678 0.6808478 0.04001638
## 36: 0.005027291 -1.1453678 0.6808478 0.04001638
## 37: 0.005027291 -1.1453678 0.6808478 0.04001638
## 38: 0.005027291 -1.1453678 0.6808478 0.04001638
## 39: 0.004876780 -1.6233205 0.9970391 0.31825293
## 40: 0.004876780 -1.6233205 0.9970391 0.31825293
## 41: 0.004864578 -1.8164413 1.1545088 0.27283204
## 42: 0.004864578 -1.8164413 1.1545088 0.27283204
## 43: 0.004864578 -1.8164413 1.1545088 0.27283204
## 44: 0.004864578 -1.8164413 1.1545088 0.27283204
## 45: 0.004864578 -1.8164413 1.1545088 0.27283204
## 46: 0.004864578 -1.8164413 1.1545088 0.27283204
## 47: 0.004864578 -1.8164413 1.1545088 0.27283204
## 48: 0.004864578 -1.8164413 1.1545088 0.27283204
## 49: 0.004864578 -1.8164413 1.1545088 0.27283204
## 50: 0.004864578 -1.8164413 1.1545088 0.27283204
## 51: 0.004864578 -1.8164413 1.1545088 0.27283204
## 52: 0.004864578 -1.8164413 1.1545088 0.27283204
## 53: 0.004864578 -1.8164413 1.1545088 0.27283204
## 54: 0.004864578 -1.8164413 1.1545088 0.27283204
## 55: 0.004864578 -1.8164413 1.1545088 0.27283204
## 56: 0.004864578 -1.8164413 1.1545088 0.27283204
## 57: 0.004864578 -1.8164413 1.1545088 0.27283204
## 58: 0.004864578 -1.8164413 1.1545088 0.27283204
## 59: 0.004864578 -1.8164413 1.1545088 0.27283204
## 60: 0.004864578 -1.8164413 1.1545088 0.27283204
## 61: 0.004864578 -1.8164413 1.1545088 0.27283204
## 62: 0.004864578 -1.8164413 1.1545088 0.27283204
## 63: 0.004864578 -1.8164413 1.1545088 0.27283204
## 64: 0.004541086 -0.4455417 1.1235184 0.24166784
## 65: 0.004541086 -0.4455417 1.1235184 0.24166784
## 66: 0.004541086 -0.4455417 1.1235184 0.24166784
## 67: 0.004541086 -0.4455417 1.1235184 0.24166784
## 68: 0.004541086 -0.4455417 1.1235184 0.24166784
## 69: 0.004541086 -0.4455417 1.1235184 0.24166784
## 70: 0.004541086 -0.4455417 1.1235184 0.24166784
## 71: 0.004541086 -0.4455417 1.1235184 0.24166784
## 72: 0.004541086 -0.4455417 1.1235184 0.24166784
## 73: 0.004541086 -0.4455417 1.1235184 0.24166784
## 74: 0.004541086 -0.4455417 1.1235184 0.24166784
## 75: 0.004541086 -0.4455417 1.1235184 0.24166784
## 76: 0.004541086 -0.4455417 1.1235184 0.24166784
## 77: 0.005235761 -1.1178069 0.8390202 0.58404011
## 78: 0.005006845 -1.4458246 0.9223899 0.99714609
## 79: 0.005006845 -1.4458246 0.9223899 0.99714609
## se.bp v c pchi
## [1] "ORF67_1" "ORF9" "ORF73" "ORF27" "ORF32" "ORF62"## [1] 6## [1] "ORF12" "ORF13" "ORF15" "ORF16" "ORF35" "ORF41" "ORF48" "ORF52" "ORF54"
## [10] "ORF57" "ORF60" "ORF71" "ORF72"## [1] 13Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 3 ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27: 3 ORF7 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28: 3 ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29: 3 ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30: 3 ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31: 3 ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32: 3 ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33: 3 ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34: 3 ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35: 3 ORF56 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 36: 3 ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 37: 3 NOIR_1 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 38: 4 ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 39: 4 ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 40: 5 ORF8 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 41: 5 ORF22 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 42: 5 ORF23 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 43: 5 ORF24 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 44: 5 ORF25 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 45: 5 ORF33 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 46: 5 ORF35.5 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 47: 5 ORF36 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 48: 5 ORF39 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 49: 5 CTO 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 50: 5 ORF40 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 51: 5 ORF42 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 52: 5 ORF43 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 53: 5 ORF44 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 54: 5 ORF46 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 55: 5 ORF49 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 56: 5 ORF58 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 57: 5 ORF62 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 58: 5 ORF68 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 59: 5 ORF74 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 60: 6 ORF12 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 61: 6 ORF13 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 62: 6 ORF15 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 63: 6 ORF16 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 64: 6 ORF35 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 65: 6 ORF41 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 66: 6 ORF48 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 67: 6 ORF52 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 68: 6 ORF54 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 69: 6 ORF57 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 70: 6 ORF60 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 71: 6 ORF71 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 72: 6 ORF72 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 73: 7 ORF27 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 74: 7 ORF32 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 75: 7 ORF59 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 76: 8 ORF28 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 77: 9 ORF45 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 78: 10 ORF64_1 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 79: 10 ORF75 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004876780 -1.6233205 0.9970391 0.31825293
## 36: 0.004876780 -1.6233205 0.9970391 0.31825293
## 37: 0.004876780 -1.6233205 0.9970391 0.31825293
## 38: 0.004864578 -1.8164413 1.1545088 0.27283204
## 39: 0.004864578 -1.8164413 1.1545088 0.27283204
## 40: 0.004541086 -0.4455417 1.1235184 0.24166784
## 41: 0.004541086 -0.4455417 1.1235184 0.24166784
## 42: 0.004541086 -0.4455417 1.1235184 0.24166784
## 43: 0.004541086 -0.4455417 1.1235184 0.24166784
## 44: 0.004541086 -0.4455417 1.1235184 0.24166784
## 45: 0.004541086 -0.4455417 1.1235184 0.24166784
## 46: 0.004541086 -0.4455417 1.1235184 0.24166784
## 47: 0.004541086 -0.4455417 1.1235184 0.24166784
## 48: 0.004541086 -0.4455417 1.1235184 0.24166784
## 49: 0.004541086 -0.4455417 1.1235184 0.24166784
## 50: 0.004541086 -0.4455417 1.1235184 0.24166784
## 51: 0.004541086 -0.4455417 1.1235184 0.24166784
## 52: 0.004541086 -0.4455417 1.1235184 0.24166784
## 53: 0.004541086 -0.4455417 1.1235184 0.24166784
## 54: 0.004541086 -0.4455417 1.1235184 0.24166784
## 55: 0.004541086 -0.4455417 1.1235184 0.24166784
## 56: 0.004541086 -0.4455417 1.1235184 0.24166784
## 57: 0.004541086 -0.4455417 1.1235184 0.24166784
## 58: 0.004541086 -0.4455417 1.1235184 0.24166784
## 59: 0.004541086 -0.4455417 1.1235184 0.24166784
## 60: 0.005235761 -1.1178069 0.8390202 0.58404011
## 61: 0.005235761 -1.1178069 0.8390202 0.58404011
## 62: 0.005235761 -1.1178069 0.8390202 0.58404011
## 63: 0.005235761 -1.1178069 0.8390202 0.58404011
## 64: 0.005235761 -1.1178069 0.8390202 0.58404011
## 65: 0.005235761 -1.1178069 0.8390202 0.58404011
## 66: 0.005235761 -1.1178069 0.8390202 0.58404011
## 67: 0.005235761 -1.1178069 0.8390202 0.58404011
## 68: 0.005235761 -1.1178069 0.8390202 0.58404011
## 69: 0.005235761 -1.1178069 0.8390202 0.58404011
## 70: 0.005235761 -1.1178069 0.8390202 0.58404011
## 71: 0.005235761 -1.1178069 0.8390202 0.58404011
## 72: 0.005235761 -1.1178069 0.8390202 0.58404011
## 73: 0.005006845 -1.4458246 0.9223899 0.99714609
## 74: 0.005006845 -1.4458246 0.9223899 0.99714609
## 75: 0.005006845 -1.4458246 0.9223899 0.99714609
## 76: 0.005251022 -0.8623157 1.0323182 0.09873270
## 77: 0.004974233 -0.4844516 0.9061108 0.88802579
## 78: 0.005408057 -1.4764202 1.4415684 0.99966378
## 79: 0.005408057 -1.4764202 1.4415684 0.99966378
## se.bp v c pchi
## [1] "ORF55" "ORF73" "ORF62" "ORF27" "ORF32" "ORF59"## [1] 6## [1] "ORF8" "ORF22" "ORF23" "ORF24" "ORF25" "ORF33" "ORF35.5"
## [8] "ORF36" "ORF39" "CTO" "ORF40" "ORF42" "ORF43" "ORF44"
## [15] "ORF46" "ORF49" "ORF58" "ORF62" "ORF68" "ORF74" "ORF45"## [1] 21Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 3 ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27: 3 ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28: 3 ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29: 3 ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30: 3 ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31: 3 ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32: 3 ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33: 3 ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34: 3 ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35: 4 ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 36: 4 ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 37: 5 ORF7 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 38: 5 ORF56 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 39: 5 NOIR_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 40: 6 ORF8 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 41: 6 ORF22 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 42: 6 ORF23 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 43: 6 ORF24 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 44: 6 ORF25 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 45: 6 ORF33 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 46: 6 ORF35.5 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 47: 6 ORF36 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 48: 6 ORF39 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 49: 6 CTO 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 50: 6 ORF40 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 51: 6 ORF42 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 52: 6 ORF43 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 53: 6 ORF44 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 54: 6 ORF46 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 55: 6 ORF49 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 56: 6 ORF58 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 57: 6 ORF62 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 58: 6 ORF68 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 59: 6 ORF74 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 60: 7 ORF12 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 61: 7 ORF13 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 62: 7 ORF15 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 63: 7 ORF16 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 64: 7 ORF35 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 65: 7 ORF41 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 66: 7 ORF48 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 67: 7 ORF52 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 68: 7 ORF54 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 69: 7 ORF57 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 70: 7 ORF60 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 71: 7 ORF71 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 72: 7 ORF72 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 73: 8 ORF27 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 74: 8 ORF59 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 75: 9 ORF28 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 76: 10 ORF32 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 77: 11 ORF45 0.7410838 0.9752328 0.2580276 0.035672004 0.0053794818
## 78: 12 ORF64_1 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## 79: 12 ORF75 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004864578 -1.8164413 1.1545088 0.27283204
## 36: 0.004864578 -1.8164413 1.1545088 0.27283204
## 37: 0.004541086 -0.4455417 1.1235184 0.24166784
## 38: 0.004541086 -0.4455417 1.1235184 0.24166784
## 39: 0.004541086 -0.4455417 1.1235184 0.24166784
## 40: 0.005235761 -1.1178069 0.8390202 0.58404011
## 41: 0.005235761 -1.1178069 0.8390202 0.58404011
## 42: 0.005235761 -1.1178069 0.8390202 0.58404011
## 43: 0.005235761 -1.1178069 0.8390202 0.58404011
## 44: 0.005235761 -1.1178069 0.8390202 0.58404011
## 45: 0.005235761 -1.1178069 0.8390202 0.58404011
## 46: 0.005235761 -1.1178069 0.8390202 0.58404011
## 47: 0.005235761 -1.1178069 0.8390202 0.58404011
## 48: 0.005235761 -1.1178069 0.8390202 0.58404011
## 49: 0.005235761 -1.1178069 0.8390202 0.58404011
## 50: 0.005235761 -1.1178069 0.8390202 0.58404011
## 51: 0.005235761 -1.1178069 0.8390202 0.58404011
## 52: 0.005235761 -1.1178069 0.8390202 0.58404011
## 53: 0.005235761 -1.1178069 0.8390202 0.58404011
## 54: 0.005235761 -1.1178069 0.8390202 0.58404011
## 55: 0.005235761 -1.1178069 0.8390202 0.58404011
## 56: 0.005235761 -1.1178069 0.8390202 0.58404011
## 57: 0.005235761 -1.1178069 0.8390202 0.58404011
## 58: 0.005235761 -1.1178069 0.8390202 0.58404011
## 59: 0.005235761 -1.1178069 0.8390202 0.58404011
## 60: 0.005006845 -1.4458246 0.9223899 0.99714609
## 61: 0.005006845 -1.4458246 0.9223899 0.99714609
## 62: 0.005006845 -1.4458246 0.9223899 0.99714609
## 63: 0.005006845 -1.4458246 0.9223899 0.99714609
## 64: 0.005006845 -1.4458246 0.9223899 0.99714609
## 65: 0.005006845 -1.4458246 0.9223899 0.99714609
## 66: 0.005006845 -1.4458246 0.9223899 0.99714609
## 67: 0.005006845 -1.4458246 0.9223899 0.99714609
## 68: 0.005006845 -1.4458246 0.9223899 0.99714609
## 69: 0.005006845 -1.4458246 0.9223899 0.99714609
## 70: 0.005006845 -1.4458246 0.9223899 0.99714609
## 71: 0.005006845 -1.4458246 0.9223899 0.99714609
## 72: 0.005006845 -1.4458246 0.9223899 0.99714609
## 73: 0.005251022 -0.8623157 1.0323182 0.09873270
## 74: 0.005251022 -0.8623157 1.0323182 0.09873270
## 75: 0.004974233 -0.4844516 0.9061108 0.88802579
## 76: 0.005408057 -1.4764202 1.4415684 0.99966378
## 77: 0.004607497 -0.6572623 1.3067005 0.59272477
## 78: 0.004713028 -0.4001193 0.9858138 0.57239618
## 79: 0.004713028 -0.4001193 0.9858138 0.57239618
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp se.si se.au
## <int> <char> <num> <num> <num> <num> <num>
## 1: 1 ORF1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 2: 1 ORF5 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 3: 1 ORF10 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 4: 1 ORF17 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 5: 1 ORF30 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 6: 1 ORF53 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 7: 1 ORF63 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 8: 1 ORF65_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 9: 1 ORF67_1 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 10: 1 ORF69 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 11: 1 NOIR_2 0.9852332 0.9975553 0.8079736 0.003147009 0.0006657068
## 12: 2 ORF2 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 13: 2 ORF3 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 14: 2 ORF11 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 15: 2 ORF14 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 16: 2 ORF18 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 17: 2 ORF19 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 18: 2 ORF26 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 19: 2 ORF29 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 20: 2 ORF37 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 21: 2 ORF51 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 22: 2 ORF55 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 23: 2 ORF66_1 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 24: 2 ORF73 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 25: 2 ORF76 0.8632617 0.9660911 0.6788624 0.017742332 0.0059885681
## 26: 3 ORF4 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 27: 3 ORF9 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 28: 3 ORF20 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 29: 3 ORF21 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 30: 3 ORF31 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 31: 3 ORF34 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 32: 3 ORF38 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 33: 3 ORF50 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 34: 3 ORF61 0.9724429 0.9956081 0.7344348 0.005118652 0.0010695938
## 35: 4 ORF6 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 36: 4 ORF70 0.9880431 0.9985156 0.7459928 0.002534594 0.0004091247
## 37: 5 ORF7 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 38: 5 ORF56 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 39: 5 NOIR_1 0.5534986 0.9416830 0.2488932 0.049652772 0.0106206584
## 40: 6 ORF8 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 41: 6 ORF22 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 42: 6 ORF23 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 43: 6 ORF24 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 44: 6 ORF25 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 45: 6 ORF33 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 46: 6 ORF35.5 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 47: 6 ORF36 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 48: 6 ORF39 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 49: 6 CTO 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 50: 6 ORF40 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 51: 6 ORF42 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 52: 6 ORF43 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 53: 6 ORF44 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 54: 6 ORF46 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 55: 6 ORF49 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 56: 6 ORF58 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 57: 6 ORF62 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 58: 6 ORF68 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 59: 6 ORF74 0.8745378 0.9748161 0.6097958 0.016704529 0.0046455437
## 60: 7 ORF12 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 61: 7 ORF13 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 62: 7 ORF15 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 63: 7 ORF16 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 64: 7 ORF35 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 65: 7 ORF41 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 66: 7 ORF48 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 67: 7 ORF52 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 68: 7 ORF54 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 69: 7 ORF57 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 70: 7 ORF60 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 71: 7 ORF71 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 72: 7 ORF72 0.9498375 0.9910629 0.6996641 0.008272803 0.0019621239
## 73: 8 ORF27 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 74: 8 ORF59 0.8074313 0.9709295 0.4325041 0.024405241 0.0054326181
## 75: 9 ORF28 0.5495521 0.9178209 0.3366369 0.043514069 0.0126360450
## 76: 10 ORF32 0.9764230 0.9982385 0.5139011 0.004566350 0.0004728576
## 77: 11 ORF45 0.7410838 0.9752328 0.2580276 0.035672004 0.0053794818
## 78: 12 ORF64_1 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## 79: 12 ORF75 0.4887267 0.9171163 0.2790404 0.049783507 0.0132393035
## cluster gene si au bp se.si se.au
## se.bp v c pchi
## <num> <num> <num> <num>
## 1: 0.004437298 -1.8423439 0.9718909 0.80502549
## 2: 0.004437298 -1.8423439 0.9718909 0.80502549
## 3: 0.004437298 -1.8423439 0.9718909 0.80502549
## 4: 0.004437298 -1.8423439 0.9718909 0.80502549
## 5: 0.004437298 -1.8423439 0.9718909 0.80502549
## 6: 0.004437298 -1.8423439 0.9718909 0.80502549
## 7: 0.004437298 -1.8423439 0.9718909 0.80502549
## 8: 0.004437298 -1.8423439 0.9718909 0.80502549
## 9: 0.004437298 -1.8423439 0.9718909 0.80502549
## 10: 0.004437298 -1.8423439 0.9718909 0.80502549
## 11: 0.004437298 -1.8423439 0.9718909 0.80502549
## 12: 0.005027291 -1.1453678 0.6808478 0.04001638
## 13: 0.005027291 -1.1453678 0.6808478 0.04001638
## 14: 0.005027291 -1.1453678 0.6808478 0.04001638
## 15: 0.005027291 -1.1453678 0.6808478 0.04001638
## 16: 0.005027291 -1.1453678 0.6808478 0.04001638
## 17: 0.005027291 -1.1453678 0.6808478 0.04001638
## 18: 0.005027291 -1.1453678 0.6808478 0.04001638
## 19: 0.005027291 -1.1453678 0.6808478 0.04001638
## 20: 0.005027291 -1.1453678 0.6808478 0.04001638
## 21: 0.005027291 -1.1453678 0.6808478 0.04001638
## 22: 0.005027291 -1.1453678 0.6808478 0.04001638
## 23: 0.005027291 -1.1453678 0.6808478 0.04001638
## 24: 0.005027291 -1.1453678 0.6808478 0.04001638
## 25: 0.005027291 -1.1453678 0.6808478 0.04001638
## 26: 0.004876780 -1.6233205 0.9970391 0.31825293
## 27: 0.004876780 -1.6233205 0.9970391 0.31825293
## 28: 0.004876780 -1.6233205 0.9970391 0.31825293
## 29: 0.004876780 -1.6233205 0.9970391 0.31825293
## 30: 0.004876780 -1.6233205 0.9970391 0.31825293
## 31: 0.004876780 -1.6233205 0.9970391 0.31825293
## 32: 0.004876780 -1.6233205 0.9970391 0.31825293
## 33: 0.004876780 -1.6233205 0.9970391 0.31825293
## 34: 0.004876780 -1.6233205 0.9970391 0.31825293
## 35: 0.004864578 -1.8164413 1.1545088 0.27283204
## 36: 0.004864578 -1.8164413 1.1545088 0.27283204
## 37: 0.004541086 -0.4455417 1.1235184 0.24166784
## 38: 0.004541086 -0.4455417 1.1235184 0.24166784
## 39: 0.004541086 -0.4455417 1.1235184 0.24166784
## 40: 0.005235761 -1.1178069 0.8390202 0.58404011
## 41: 0.005235761 -1.1178069 0.8390202 0.58404011
## 42: 0.005235761 -1.1178069 0.8390202 0.58404011
## 43: 0.005235761 -1.1178069 0.8390202 0.58404011
## 44: 0.005235761 -1.1178069 0.8390202 0.58404011
## 45: 0.005235761 -1.1178069 0.8390202 0.58404011
## 46: 0.005235761 -1.1178069 0.8390202 0.58404011
## 47: 0.005235761 -1.1178069 0.8390202 0.58404011
## 48: 0.005235761 -1.1178069 0.8390202 0.58404011
## 49: 0.005235761 -1.1178069 0.8390202 0.58404011
## 50: 0.005235761 -1.1178069 0.8390202 0.58404011
## 51: 0.005235761 -1.1178069 0.8390202 0.58404011
## 52: 0.005235761 -1.1178069 0.8390202 0.58404011
## 53: 0.005235761 -1.1178069 0.8390202 0.58404011
## 54: 0.005235761 -1.1178069 0.8390202 0.58404011
## 55: 0.005235761 -1.1178069 0.8390202 0.58404011
## 56: 0.005235761 -1.1178069 0.8390202 0.58404011
## 57: 0.005235761 -1.1178069 0.8390202 0.58404011
## 58: 0.005235761 -1.1178069 0.8390202 0.58404011
## 59: 0.005235761 -1.1178069 0.8390202 0.58404011
## 60: 0.005006845 -1.4458246 0.9223899 0.99714609
## 61: 0.005006845 -1.4458246 0.9223899 0.99714609
## 62: 0.005006845 -1.4458246 0.9223899 0.99714609
## 63: 0.005006845 -1.4458246 0.9223899 0.99714609
## 64: 0.005006845 -1.4458246 0.9223899 0.99714609
## 65: 0.005006845 -1.4458246 0.9223899 0.99714609
## 66: 0.005006845 -1.4458246 0.9223899 0.99714609
## 67: 0.005006845 -1.4458246 0.9223899 0.99714609
## 68: 0.005006845 -1.4458246 0.9223899 0.99714609
## 69: 0.005006845 -1.4458246 0.9223899 0.99714609
## 70: 0.005006845 -1.4458246 0.9223899 0.99714609
## 71: 0.005006845 -1.4458246 0.9223899 0.99714609
## 72: 0.005006845 -1.4458246 0.9223899 0.99714609
## 73: 0.005251022 -0.8623157 1.0323182 0.09873270
## 74: 0.005251022 -0.8623157 1.0323182 0.09873270
## 75: 0.004974233 -0.4844516 0.9061108 0.88802579
## 76: 0.005408057 -1.4764202 1.4415684 0.99966378
## 77: 0.004607497 -0.6572623 1.3067005 0.59272477
## 78: 0.004713028 -0.4001193 0.9858138 0.57239618
## 79: 0.004713028 -0.4001193 0.9858138 0.57239618
## se.bp v c pchi
## [1] "NOIR_2" "ORF1" "ORF55" "ORF73" "ORF62"## [1] 5## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6Remove genes from clusters ?
## [1] "ORF7" "ORF56" "NOIR_1" "ORF28" "ORF64_1" "ORF75"## [1] 6## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 6 20
## 2: 2 14
## 3: 7 13
## 4: 1 11
## 5: 3 9
## 6: 5 3
## 7: 4 2
## 8: 8 2
## 9: 12 2
## 10: 9 1
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
